Method for Obtaining Aptamers

ABSTRACT

The invention relates to a new method for obtaining aptamers directed against protein targets comprising a histidine-containing surface domain, and aptamers obtaining by said method.

FIELD OF THE INVENTION

The instant patent application relates to improved methods for obtainingaptamers directed against proteins such as fibrinogen andimmunoglobulins.

BACKGROUND OF THE INVENTION

Aptamers are synthetic, single-stranded polynucleotides having unique3-D structures allowing them to bind specifically to other targetmolecules. Aptamers generally exhibit high affinity for their targetwith Kd values in the low nanomolar to picomolar range.

Aptamers are routinely identified through process called SystematicEvolution of Ligands by Exponential enrichment (SELEX). All SELEX-basedprocesses comprise common sequential steps: The processes begin by thegeneration of a large and random library of about 10¹² to 10¹⁵ DNA orRNA molecules. The random library is incubated directly with the target,whereby certain oligonucleotides of the library specifically bind to thetarget. The target-binding oligonucleotides are separated fromnonbinding oligonucleotides, eluted and amplified by PCR (for DNA SELEX)or RT-PCR (for RNA SELEX) so as to generate a new and enriched pool ofselected oligonucleotides. Iterative rounds of selection andamplification are performed until the target-interacting sequencesdominate the population. Typically from 6 to 18 iterative cycles ofselection and amplification are needed to obtain aptamers with suitableaffinity to the target (Proske, Appl Microbiol. Biotechonol, 2005,69:367-374, Stolienburg et al., Biomolecular Engineering, 2007, 24,381-403). Additional steps can be introduced into each round of theprocess in order to control the binding properties of theoligonucleotides. For instance, negative selection steps can beintroduced in order to remove aptamers which cross-react with anotherprotein or in order to direct the selection to aptamers binding to aspecific epitope of the target. Over the last decade, SELEX technologyenabled the identification of aptamers directed against a wide varietyof targets such as small molecules, peptides and proteins, includingcell membranes proteins. Despite SELEX processes are all based on thesame principle, there is no standardized SELEX protocol which would workfor any target. The SELEX design and the conditions to use, inparticular in the selection step, depend on the target, the compositionof the starting library, and the desired features sought for theaptamers in terms of affinity, selectivity and potential application.

As of today, the identification of aptamers directed against certainprotein targets remain a real challenge. The success rate of basic SELEXis less than 30%. Indeed, certain proteins, such as fibrinogen orimmunoglobulin, are resistant to SELEX process, whereby theidentification of aptamers directed against these proteins is verydifficult and even impossible, starting from natural oligonucleotidelibraries or 2′-O-modified RNA libraries.

The limited chemical diversity of oligonucleotide libraries has beensuspected as the main cause explaining the low rate of success of basicSELEX. Gold and coll. thus suggest introducing chemically-modifiednucleotides comprising functional groups which mimic side-chains ofamino acids. They built chemically-modified oligonucleotides comprising5-modified deoxyuridine with hydrophobic groups such as alkyl chains andaromatic groups. The use of such libraries made a dramatic difference interms of success rate of SELEX: Gold and coll. enabled to obtain successrates of about 80%, and identified chemically-modified aptamers with Kdof the nM range directed against different resistant-SELEX proteins.These aptamers called SOMAmers (for Slow Off-rate Modified Aptamers) arecharacterized by high koff. The interactions between the SOMAmers andtheir target are less polar and more hydrophobic as compared toconventional aptamers (Rohloff et al., Molecular Therapy-Nucleic Acids,2014, 3, e201).

However, despite the high rate of success, 5-modified deoxyuridinelibraries have several drawbacks. There is no universal chemicallymodified oligonucleotide library which enables to identify appropriateSOMAmers for any target. Indeed, the chemically modified library to usefor a given target (i.e. the type of functional moiety to introduce onthe backbone of nucleotides) cannot be predicted a priori, whereby for agiven target, it may be necessary to randomly perform several SELEXprocesses from several different starting libraries in order to identifythe appropriate starting library to use. Moreover, such SELEX technologyis more demanding and more costly to implement. At last, SOMAmers arenot suitable to be used as affinity ligands in purification because oftheir binding property that are not likely to allow elution of theprotein target in mild and selective elution conditions.

There is thus a need for an alternative SELEX process enabling toidentify aptamers directed against SELEX-resistant proteins and whichwould be suitable for use in purification.

SUMMARY OF THE INVENTION

The invention relates to a method for obtaining an aptamer against aprotein target comprising a histidine-containing surface domain, saidmethod comprising:

-   -   a) contacting the protein target with a candidate mixture of        nucleic acids at a pH promoting the formation of positive charge        on the histidine-containing surface domain of said protein        target,    -   b) recovering nucleic acids which bind to the protein target,        while removing unbound nucleic acids,    -   c) amplifying the nucleic acids obtained in step (b) to yield to        a candidate mixture of nucleic acids with increased affinity to        the protein target, and    -   d) repeating steps (a), (b), (c) until obtaining one or several        aptamers against the protein target of interest.

In some embodiments, the pH in step a) is less than 7.0, preferably from5.0 to 6.9. In some other or additional embodiments, the pH in step a)is selected so that the electrostatic surface potential of ahistidine-containing surface domain of the protein target is positive.

In some other embodiments, the pH of step (a) is determined by obtainingsurface electrostatic potential maps at different pH and selecting a pHwhich enables to obtain a positive surface potential on at least onehistidine-containing surface domain of the protein target and which isincluded in the stability range of the protein target.

The protein target may comprise at least one of the following feature:

-   -   the protein target has an isoelectric point (pI) of less than        7.5, preferably less than 7.0 and/or    -   the protein target is devoid of any surface domain with positive        electrostatic potential at a pH of more than 7.0.

In some embodiments, the protein target is selected from the groupconsisting of fibrinogen, immunoglobulin, Fc fragment, and variantsthereof.

In step a), the candidate mixture may consist of a multitude ofsingle-stranded DNAs.

In some further embodiments, step b) comprises the sub-steps of

-   -   separating the complex formed in step (a) from unbound nucleic        acids, and    -   releasing the nucleic acids from the complex, wherein the        dissociation of the complex between the bound nucleic acids and        the protein target is performed by increasing the pH at a value        higher than that used in step a), preferably of a ΔpH of at        least 0.8.

In certain embodiments, the method of the invention may comprise thesteps of

-   -   i. sequencing an aptamer obtained in step (c),    -   ii. optionally optimizing the sequence of said aptamer, and    -   iii. producing the aptamer, preferably by chemical synthesis.

In another aspect, the invention relates to an aptamer obtainable orobtained by the method as defined above. Preferably, the aptamer bindsto a protein target comprising a histidine-containing surface domain ina pH dependent-manner For instance, the aptamer of the invention bindsto the protein target at an acidic pH, preferably selected from 5.0 to6.5, but does not bind to the protein target at a pH of more than 7.0.

The invention also relates to an affinity ligand which comprises anaptamer of the invention and at least one moiety for immobilization ontoa support. An additional object of the invention is an affinity supportcomprising thereon a plurality of aptamers or a plurality of affinityligands as defined above.

An additional object of the invention is a method for obtaining anaptamer against a protein target said method comprising:

-   -   (i) determining a pH value promoting positive charges in at        least one surface domain of the protein target,    -   (a) contacting the protein target with a candidate mixture of        nucleic acids at the pH determined in step (i) in conditions        favourable for binding of the protein target with nucleic acids        having affinity for said targets,    -   (b) recovering nucleic acids which bind to the protein target,        while removing unbound nucleic acids,    -   (c) amplifying the nucleic acids obtained in step (b) to yield        to a candidate mixture of nucleic acids with increased affinity        to the protein target, and    -   (d) repeating steps (a), (b), (c) until obtaining one or several        aptamers against the protein target of interest.

In some embodiments, said method of claim comprises the steps of:

-   -   determining the presence of a histidine-containing surface        domain in the protein target, and    -   if said domain is present, determining a pH value promoting        positive charges, preferably enabling to obtain a local positive        surface electrostatic potential, in said histidine-containing        surface domain.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows the three-dimensional structure of human fibrinogen. Thesurface histidine are indicated in dark. Eighteen histidines aredistributed over the surface of homodimeric fibrinogen with aninter-histidine distance between 10-65 Angstrom.

FIG. 1B shows the three-dimensional structure of homodimeric Fc of humanIgG. The surface histidines of one of the monomers are shown in dark.There are four surface histidines per monomer. Three surface histidines(H433, H435, H310) are positioned in a close linear arrangement with aninter -histidine distance of 10 Angstrom. The fourth histidine is at adistance of 22 Angstrom from the closest of the tree others histidines.The surface histidines of the second monomer are on the backside.

FIG. 2 shows the protocol of the SELEX according to the invention usedto identify aptamers directed against human fibrinogen.

FIGS. 3-4 show the binding properties of some aptamers directed againsthuman fibrinogen obtained by the method of the invention:

FIG. 3A shows the SPR binding curves of human plasma fibrinogen presentat a concentration from 125 nM to 1000 nM on SEQ ID NO: 3 (the coresequence of SEQ ID NO:1) immobilized on a chip. Each solution of humanplasma fibrinogen was injected at pH 6.3 whereby a complex was formed ina dose-dependent manner as evidenced by the increase of the signalsdepending on the concentration of fibrinogen. The injection of a buffersolution at pH 6.3 comprising 0.5 M NaCl did not significantly inducethe elution of human plasma fibrinogen. Fibrinogen was then releasedfrom the complex by an elution buffer at pH 7.40. The solid support wasthen regenerated by injecting a solution of NaOH at 50 mM. X-axis: timein s. Y-axis: SPR response in arbitrary scale.

FIG. 3B shows the SPR binding curves of transgenic fibrinogen present ata concentration from 125 nM to 1000 nM on SEQ ID NO: 3 (the coresequence of SEQ ID NO:1) immobilized on a chip. Each solution oftransgenic fibrinogen was injected at pH 6.3 whereby a complex wasformed in a dose-dependent manner as evidenced by the increase of thesignals depending on the concentration of fibrinogen. The injection of abuffer solution at pH 6.3 comprising 0.5 M NaCl did not significantlyinduce the elution of transgenic fibrinogen. Fibrinogen was thenreleased from the complex by an elution buffer at pH 7.40. The solidsupport was then regenerated by injecting a solution of NaOH at 50 mM.X-axis: time in s. Y-axis: SPR response in arbitrary scale

FIG. 3C shows the SPR binding curves of human plasma fibrinogen presentat a concentration from 125 nM to 1000 nM on SEQ ID NO: 4 (the coresequence of SEQ ID NO:2) immobilized on a chip. Each solution of humanplasma fibrinogen was injected at pH 6.3 whereby a complex was formed ina dose-dependent manner as evidenced by the increase of the signalsdepending on the concentration of fibrinogen. The injection of a buffersolution at pH 6.3 comprising 1 M NaCl did not considerably induce theelution of human plasma fibrinogen. Fibrinogen was then released fromthe complex by an elution buffer at pH 7.40 and containing MgCl2 at 2M.The solid support was then regenerated by injecting a solution of NaOHat 50 mM. X-axis: time in s. Y-axis: SPR response in arbitrary scale.

FIG. 3D shows the SPR binding curves of transgenic fibrinogen present ata concentration from 125 nM to 1000 nM on SEQ ID NO: 4 (the coresequence of SEQ ID NO:2) immobilized on a chip. Each solution oftransgenic fibrinogen was injected at pH 6.3 whereby a complex wasformed in a dose-dependent manner as evidenced by the increase of thesignals depending on the concentration of fibrinogen. The injection of abuffer solution at pH 6.3 comprising 1 M NaCl did not considerablyinduce the elution of transgenic fibrinogen. Fibrinogen was thenreleased from the complex by an elution buffer at pH 7.40 and containingMgCl2 at 2M. The solid support was then regenerated by injecting asolution of NaOH at 50 mM. X-axis: time in s. Y-axis: SPR response inarbitrary scale.

FIG. 4A shows SPR sensograms illustrating the pH dependency of bindingof fibrinogen to immobilised aptamer SEQ ID NO:3 (the core sequence ofSEQ ID NO:1). Plasmatic Fibrinogen is injected at different pH, aftersample injection a running buffer at pH 6.30 is passed over the flowcell in every run. The highest binding level is obtained for pH 6.30.The binding level decreases when pH increases. X-axis: time in s.Y-axis: SPR response in arbitrary scale.

FIG. 4B shows SPR sensograms illustrating the pH dependency of bindingaffinity of aptamer of SEQ ID NO: 4 (the core sequence of SEQ ID NO:2)to human plasma fibrinogen. No binding is observed for pH higher than6.8. X-axis: time in s. Y-axis: SPR response in arbitrary scale.

FIG. 5A shows the chromatographic profile for the purification offibrinogen on an affinity support grafted with aptamer of SEQ ID NO:3.Y-axis: absorbance at 280 nm. X-axis: in mL

FIG. 5B shows the picture of the electrophoresis gels after coomassieblue staining in non-reduced conditions. From left to right: 1: plasma,2: fraction from the plasma which was not retained on the stationaryphase, 3: elution fraction containing fibrinogen obtained from thechromatography of plasma, 4: fraction obtained after regeneration of thestationary support, and 5: molecular weight markers. The purity of theelution fraction for fibrinogen was more than 95% as compared to thetotal amount of proteins contained in the fraction. The affinity supportused in chromatography was grafted with aptamers of SEQ ID NO:3.

FIG. 6A shows the chromatographic profile for the purification offibrinogen from plasma on an affinity support grafted with aptamer ofSEQ ID NO:4. Y-axis: absorbance at 280 nm. X-axis: in mL

FIG. 6B shows the picture of the electrophoresis gels after coomassieblue staining in non-reduced conditions. From left to right: 1: plasma,2: fraction from the plasma which was not retained on the stationaryphase, 3: fraction obtained after washing of the stationary support, 4:elution fraction containing fibrinogen obtained from the chromatographyof plasma, and 5: molecular weight markers. The purity of the elutionfraction for fibrinogen was of least 95% as compared to the total amountof proteins contained in the fraction. The affinity support used inchromatography was grafted with aptamers of SEQ ID NO:4.

FIG. 7A shows the chromatographic profile obtained for the purificationof semi-purified fibrinogen on an affinity support grafted with aptamerof SEQ ID NO:3. Y-axis: absorbance at 280 nm. X-axis: in mL

FIG. 7B shows the chromatographic profile obtained for the purificationof semi-purified fibrinogen on an affinity support grafted with aptamerof SEQ ID NO:4. Y-axis: absorbance at 280 nm. X-axis: in mL.

FIGS. 7C shows the analysis of the fractions by SDS-PAGE in reduced andnon-reduced conditions, with AgNO3 staining, of the elution fractionsobtained by purification of intermediate fibrinogen on the affinitysupports. Lane 1: molecular weight standard. Lane 2: Fibrinogenintermediate (starting material), Lane 3: Elution fraction obtained withaffinity support n° 1 (aptamers of SEQ ID NO:3), Lane 4: Elutionfraction obtained with affinity support n° 2 (aptamers of SEQ ID NO:4)

FIGS. 7D shows the analysis of the fractions by SDS-PAGE in reduced andnon-reduced conditions, with coomassie staining, of the elutionfractions obtained by purification of intermediate fibrinogen on theaffinity supports. Lane 1: molecular weight standard. Lane 2,3:Fibrinogen intermediate (starting material), Lane 4,5: Elution fractionobtained with affinity support n° 1 (aptamers of SEQ ID NO:3), Lane 6,7:Elution fraction obtained with affinity support n° 2 (aptamers of SEQ IDNO:4). NR: non reduced. R: Reduced.

FIG. 8 shows the SELEX protocol used to identify aptamers directedagainst Fc fragment of human IgG.

FIGS. 9 show the binding properties of some aptamers directed againsthuman Fc fragment obtained by the method of the invention:

FIG. 9A shows the binding curves of human polyclonal IgG (sensorgram)for aptamers of SEQ ID NO:5 (A6-2) and SEQ ID NO:6 (A6-8) immobilized ona sensor chip, obtained by SPR technology. Purified (>95%) humanpolyclonal IgG (200 nM) was injected at pH 5.50, whereby a complex wasformed as evidenced by the increase of the signal. The injection of abuffer solution at pH 5.50 comprising 2M NaCl did not significantlyinduce the elution of human polyclonal IgG. Human polyclonal IgG wasthen released from the complex by an elution buffer at pH 7.40. Thesolid support was then regenerated by injecting a solution of NaOH at 50mM. X-axis: time in s. Y-axis: SPR response in arbitrary scale

FIG. 9B shows SPR sensograms illustrating the pH dependency of bindingof polyclonal IgG to immobilised aptamer A6-2. Polyclonal IgG isinjected at different pH (in duplicates), after sample injection arunning buffer at pH 5.50 is passed over the flow cell in every run. Thehighest binding level is obtained for pH 5.30. The binding leveldecreases when pH increases. X-axis: time in s. Y-axis: SPR response inarbitrary scale.

FIG. 10A shows the chromatographic profiles for plasma and pre-purifiedIgG on an affinity support grafted with aptamer of SEQ ID NO:5. Y-axis:absorbance at 280 nm. X-axis: in mL

FIG. 10B shows the picture of the electrophoresis gel after coomassieblue staining. From left to right: 1: human plasma, 2: fraction from theplasma which was not retained on the stationary phase, 3: elutionfraction containing IgGs obtained from the chromatography of plasma, 4:positive control (plasma IgG) and 5: molecular weight markers.

FIG. 11A shows the binding curves of human plasmatic and transgenicfibrinogen (sensorgram) for an aptamer from Base Pair Biotechnologies(reference 6F01 oligo #370) immobilized on a sensor chip, obtained bySPR technology. Human plasmatic and transgenic fibrinogen (1000 nM) wasinjected at pH 7.40 using the Base Pair Biotechnologies recommendedbuffer. Very low binding levels were observed for human plasmatic andtransgenic fibrinogen. The solid support was then regenerated byinjecting a solution of NaOH at 50 mM. X-axis: time in s. Y-axis: SPRresponse in arbitrary scale.

FIG. 11B shows the binding curve of purified plasma IgG (sensorgram) foraptamer ATW0018 from Base Pair technologies using the binding bufferrecommended by the manufacturer, namely PBS buffer containing 1 mMMgCl₂. No binding was observed. X-axis: time in s. Y-axis: SPR responsein arbitrary scale.

Remarks:

MBS buffer refers to 50 mM MOPS/150 mM NaCl

MBS 1M NaCl buffer refers to 50 mM MOPS/1M NaCl

MBS-M5 buffer refers to: 50 mM MOPS/150mM NaCl/5 mM MgCl₂

MBS-M5 0.5M NaCl buffer refers to 50 mM MOPS pH 6.30/0.5M NaCl/5 mMMgCl2

DETAILED DESCRIPTION OF THE INVENTION

The success rate of SELEX processes from standard oligonucleotidelibraries is less than 30%, whereby it may be impossible to obtainaptamers directed to certain proteins having unfavourable propertieswhich might preclude strong interactions with aptamers. The use ofchemically modified libraries as described in Rohloff et al., (seesupra) has increased the success rate, but this method has severaldrawbacks. This method is time-consuming, expensive and difficult toimplement. Moreover the use of such starting libraries leads to aptamershaving binding properties which may preclude their use as affinityligands in purification technology such as chromatography.

In that context, the Applicant performed extensive researches to developa new method for obtaining aptamers directed against “SELEX-resistant”proteins.

The Applicant conceived a new SELEX process which enables to obtainaptamers displaying high binding affinity for “SELEX-resistant”proteins, and which may be used as affinity ligands in purificationprocess. This new SELEX process is characterized by a selection stepwhich is performed in conditions of pH suitable to create “positivepatches” on the surface of the protein target. In other words, theprocess conceived by the Applicant is based on the enhancement of thelocal interactions between the potential aptamers and the targetedprotein by promoting positive charges on a surface domain of theprotein. The Applicant calls this method “locally enhanced electrostaticinteraction SELEX”.

This method can be implemented in particular for proteins having one orseveral surface histidines, in particular a histidine-containing surfacedomain and known or expected to have unfavourable properties forinteractions with polyanions such as nucleic acids.

Noteworthy, the method of the invention does not require the use ofsophisticated chemically-modified oligonucleotides libraries and can beimplemented from any oligonucleotide libraries. The method of theinvention also enables to obtain aptamers displaying binding propertiessuitable for use as affinity ligands in purification process. Indeed,the method of the invention provides aptamers which specifically bind totheir target, and allows mild elution conditions in chromatographyprocess. In particular, an aptamer obtained by the method of theinvention and its targeted protein may interact in a pH-dependentmanner, whereby the release of the targeted protein from the complexformed between the aptamer and the said protein may be obtained in mildand gently conditions by adjusting the pH conditions.

The Applicants validated the method of the invention for two proteinmodels, namely fibrinogen and the Fc fragment of immunoglobulin of the Gisotype (IgG).

Certainly, aptamers which potentially bind to fibrinogen have beendescribed in the prior art. PCT application, WO2010/019847 describesaptamers directed against fibrinogen and fibrin and comprising at leastone nucleotide having a boronic moiety (i.e. a boronic acid-modifiednucleotide). US patent application 2013-0245243 in the name of Base PairTechnologies describes several potential anti-fibrinogen aptamers, butdoes not provide any evidence showing the actual affinity andspecificity of these aptamers for fibrinogen. EP 1 918 372 in the nameof Ribomic describes several RNA aptamers against IgGs.

Base Pair Biotechnologies also markets aptamers stated asanti-fibrinogen (reference 6F01 oligo #370) or anti-IgG (reference CO2oligo #369) aptamers for research use only.

The Applicants investigated the ability of said aptamers to be used asaffinity ligands for the purification of fibrinogen and IgGs. Theexperiments performed by the Applicant demonstrated that said aptamersdid not have binding properties suitable for use as affinity ligands. Asshown in FIG. 11A, the anti-fibrinogen aptamer marketed by Base PairBiotechnologies (reference 6F01 oligo #370) displayed very low bindingto both transgenic and human fibrinogen, even with the binding bufferrecommended by the manufacturer. This low binding capacity precludes itsuse as affinity ligand in purification process. Similarly, the Applicantshowed that aptamer ATW0018 marked by Base Pair technologies had a lowbinding to plasma polyclonal IgG (see FIG. 11B)

Then, the Applicants carried-out several SELEX strategies described inthe prior art to identify aptamers against human fibrinogen or humanIgG. None of these strategies succeeded. Noteworthy, SELEX processimplemented for obtaining anti-fibrinogen aptamers led to theidentification of aptamers directed against a contaminant accounting forless than 1% in the purified fibrinogen composition used forimplementing SELEX process. On the other hand, standard SELEX, performedto identify aptamers directed against the Fc fragment derived from amonoclonal IgG, also failed and led to the identification of aptamersagainst the hypervariable region of the monoclonal IgG, which waspresent in trace amounts in the Fc preparation. Noteworthy, all theSELEX strategies described in the prior art and tested by the Applicantencompass selection steps performed at physiological pH, around pH 7.5

As fully-described in the below examples, by implementing the selectionstep of SELEX process at a pH value promoting the formation of “positivepatches” on the protein target surface, for instance at pH 6.3 forfibrinogen and at pH 5.5 for IgG, the Applicant obtained severalaptamers displaying appropriate binding properties for IgG andfibrinogen, respectively, and which can be used as affinity ligands inthe purification of said proteins, even from complex medium such asplasma, at the industrial scale. Noteworthy, the aptamers obtained bythe process of the invention may bind to their protein target inpH-dependent manner Such property is particularly suitable for use inaffinity chromatography because the formation of the complex between theprotein target to purify and the aptamer, and the subsequent release ofthe protein target from the complex can be controlled by merelymodifying the pH of the elution buffer. In other words, the elution canbe performed in mild and selective conditions which are not likely todenature the protein target.

-   -   Method for Obtaining an Aptamer Against a Protein Target        Comprising a Histidine-Containing Surface Domain

In a first aspect, the invention relates to a method for obtaining anaptamer against a protein target comprising a histidine-containingsurface domain, said method comprising:

-   -   a) contacting the protein target with a candidate mixture of        nucleic acids at a pH promoting the formation of at least one        positive charge on said histidine-containing surface domain of        the protein target, and in conditions favourable for the binding        of the protein target with nucleic acids having affinity for        said target,    -   b) recovering nucleic acids which bind to the protein target,        while removing unbound nucleic acids,    -   c) amplifying the nucleic acids obtained in step (b) to yield to        a candidate mixture of nucleic acids with increased affinity to        the protein target, and    -   d) repeating steps (a), (b), (c) until obtaining one or several        aptamers against the protein target.

As used herein, an “aptamer” (also called herein “nucleic aptamer” or“nucleic ligand”) refers to a synthetic single-stranded oligonucleotidetypically comprising from 20 to 150 nucleotides in length and able tobind with high affinity to a target molecule. The aptamers arecharacterized by three-dimensional conformation(s) which may play a keyrole in their interactions with their target molecule. The interactionsbetween an aptamer and its target molecule may include electrostaticinteractions, hydrogen bonds, aromatic stacking and shapecomplementarity. The aptamer displays a high affinity for its targetmolecule. The dissociation constant (Kd) of an aptamer for its targetmolecule is typically from 10⁻⁶ to 10⁻¹² M, preferably from 10⁻⁸ to10⁻¹² M. Typically, the aptamer specifically binds to its targetmolecule. The term “specifically binding” is used herein to indicatethat the aptamer has the capacity to recognize and interact specificallywith its target molecule, while having relatively little detectablereactivity with other molecules which may be present in a sample.Preferably, the aptamer specifically binds to its target molecule if itsaffinity is significantly higher for the target molecule, as compared toother molecules, including molecules structurally close to the targetmolecule.

For instance, an aptamer might be able to specifically bind to a humanprotein while displaying a lower affinity for a homolog of said humanprotein.

As used herein, “an aptamer display a higher affinity for its targetmolecule as compared to a given molecule” or “an aptamer is specific toits target molecule as compared to a given molecule” means that thedissociation constant (Kd) of the aptamer for its target molecule is atleast 5-fold, preferably, at least 10, 20, 30, 40, 50, 100, 200, 500, or1000-fold lower than the Kd of said aptamer for the given molecule. Insome embodiments, the aptamer does not bind to the given molecule, whichmeans that the possible association of the aptamer with said givenmolecule is undetectable. Kd is preferably determined by surface plasmonresonance.

The aptamer may be a deoxyribonucleic acid (DNA) or a ribonucleic acid(RNA). The aptamer may comprise one or several chemically-modifiednucleotides as detailed further below.

As used herein, “a protein target” is virtually any protein for whichaptamers are sought. In the context of the above-detailed process, saidprotein target comprises at least one surface histidine and inparticular a histidine-containing surface domain.

As used herein, “Surface amino acids” refer to amino acid residues whichare on the surface of the protein, namely exposed to the bulk solvent.

Accordingly, “a surface histidine” refers to a histidine residue of theprotein target which is exposed to the environment and thus accessibleto the solvent. In some embodiments, said protein target may comprise atleast 2, 3, 4, 5, 6, 7, 8, 9, or 10 surface histidines.

The protein target comprises a histidine-containing surface domain,whereby in step a), the pH is selected so as to promote the formation ofpositive charges on said histidine-containing surface domain.Preferably, the pH is selected so as to protonate the at least onesurface histidine(s) present in the histidine-surface containing domain.

As used herein, “A histidine-containing surface domain” refers to asurface domain comprising at least one surface histidine residue, i.e.one histidine surface residue or several surface histidine residues. Thewording “several surface histidine residues” encompasses at least 2, 3,4, 5, 6, 7, 8, 9, or 10 histidine residues.

In some embodiments, the histidine-containing surface domain containsone single surface histidine. Indeed, one surface histidine may besufficient to promote interaction with aptamers. In other embodiments,the “histidine-containing surface domain” may contain several histidineresidues, such as 2, 3, 4 or 5. In some embodiments, such histidineresidues may be close to each other, for instance at a distance of about10-20 Angstrom.

A histidine-containing surface domain is typically a surface domain ofthe protein target containing (i) the at least one surface histidineresidue and (ii) the surface amino acid residues which are in thevicinity of the at least surface histidine. The vicinal amino acidresidues may be for instance at a distance of less than 60 (e.g. lessthan 50, 40 or 30) Angstrom of said at least one surface histidineresidue.

The histidine-containing surface domain may account for 0.5% to 60%,preferably from 0.5% to 10% of the total surface area of the targetprotein.

In some embodiments, the target protein may comprise severalhistidine-containing surface domains, for instance at least 2, 3, 4, 5,6, 7, 8, 9 or 10 histidine-containing surface domains. When the targetprotein comprises several histidine-containing surface domains, it maybe sufficient to create a positive charge on one histidine-containingsurface domain to promote interactions with aptamers. For a givenprotein, the presence of “surface histidine residue(s)” and“histidine-containing surface domain” can be determined by molecularmodelling from the primary sequence of the protein. For instance, thetertiary or quaternary structure of the protein can be predicted fromthe primary amino acid sequence by using modelling software such asModeller software (https://salilab.org/modeller/) by comparison withhomologous proteins.

Alternatively, the presence of “a histidine-containing surface domain”can also be determined from the crystalline structure of the protein.Methods for obtaining protein crystals are well-known by the skilledartisan.

In some embodiments, the histidine-containing surface domain has apositive electrostatic surface potential at a pH lower than 7.0,preferably lower than 6.5, for instance lower than 6.0. In a preferredembodiment, histidine-containing surface domain is not a HIS tag domain,e.g. a polyhistidine moiety introduced on the N-extremity or C-extremityof the protein for purification purpose.

In particular, the protein of interest may be any “SELEX-resistant”protein, i.e. any protein for which basic SELEX, i.e. SELEX processperformed on an unmodified oligonucleotide library as described inWO9119813 fails.

In some embodiments, the protein target of interest may be any proteinwhich displays unfavourable properties for interactions with polyanions,in particular with nucleic acids, at physiological pH, namely at a pHaround 7.0.

Such proteins encompass, without being limited to:

-   -   proteins having an isoelectric point (pI) of less than 7.5,        preferably less than 7.0,    -   proteins which are devoid of any surface domain with a positive        surface electrostatic potential at a pH of more than 7.0.

Generally, the pI of a given protein does not refer to a single valuebut is rather defined as a value range. For instance, the pI offibrinogen is from 5.10 to 6.3. As used herein, a protein having a pI ofless than 7.5 means that the upper value of the pI range is lower than7.5.

A protein having an isoelectric point of less than 7.5, encompasses aprotein having a pI of less than 7.4, 7.3, 7.2, 7.1, 7.0, 6.9, 6.8, 6.7,6.6, 6.5, 6.4, 6.3, 6.2, 6.1, 6.0, 5.9, 5.8, 5.7, 5.6, or 5.5. Forinstance, the, pI of the protein may be from 4.0 to 6.9.

In some embodiments, the protein of interest used in the SELEX processof the invention is devoid of any HIS tag

In some embodiments, the protein target of interest has the amino acidsequence of a human wild-type protein or is a variant or a fragment of ahuman wild-type protein.

As used herein, a variant of a wild-type protein refers to a proteinhaving at least 80% of sequence identity, preferably at least 85%, 90%,or 95% of sequence identity with said wild-type protein and whichdisplays a similar biological activity as compared to said wild-typefibrinogen. The variant may have an increased or a decreased biologicalactivity as compared to the corresponding wild-type protein. In someembodiments, the protein target is a recombinant protein, for instanceobtained from a recombinant host cell, or a recombinant pluricellularorganism, such as a transgenic animal.

In some alternate or additional embodiments, the protein target isselected from the group consisting of fibrinogen, immunoglobulins andfragments or variants thereof as well as proteins containing a Fcregion.

As used herein, “Fc”, “Fc Fragment” or “Fc region” refers to thepolypeptide comprising the constant region of an antibody excluding thefirst constant region immunoglobulin domain. Thus, Fc refers to the lasttwo constant region immunoglobulin domains of IgA, IgD, and IgG, thelast three constant region immunoglobulin domains of IgE and IgM, andthe flexible hinge N-terminal to these domains.

By “immunoglobulin” or “full-length antibodies” as used herein is meantthe structure that constitutes the natural biological form of anantibody, including variable and constant regions. “Full lengthantibody” covers monoclonal full-length antibodies, wild-typefull-length antibodies, chimeric full-length antibodies, humanizedfull-length antibodies, the list not being limitative. In most mammals,including humans and mice, the structure of full-length antibodies isgenerally a tetramer. Said tetramer is composed of two identical pairsof polypeptide chains, each pair having one “light” (typically having amolecular weight of about 25 kDa) and one “heavy” chain (typicallyhaving a molecular weight of about 50-70 kDa). In some mammals, forexample in camels and lamas, full-length antibodies may consist of onlytwo heavy chains, each heavy chain comprising a variable domain attachedto the Fc region. Such antibodies are called heavy chain antibodies.Heavy chain antibodies also encompass IgNar from cartilaginous fishes.

In some embodiments, the protein target is a protein containing a humanFc fragment, in particular an immunoglobulin, a Fc-fusion protein or aFc-conjugate.

In the case of human immunoglobulins, light chains are classified askappa and lambda light chains. Heavy chains are classified as mu, delta,gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD,IgG, IgA, and IgE, respectively. IgG has several subclasses, including,but not limited to IgG1, IgG2, IgG3, and IgG4. IgM has subclasses,including, but not limited to, IgM1 and IgM2. Thus, “isotype” as usedherein is meant any of the subclasses of immunoglobulins defined by thechemical and antigenic characteristics of their constant regions. Theknown human immunoglobulin isotypes are IgG1, IgG2, IgG3, IgG4, IgA1,IgA2, IgM1, IgM2, IgD, and IgE.

In some embodiments, the protein target may contain a Fc fragment from ahuman immunoglobulin, in particular from a IgG.

The immunoglobulin (Ig) may be a naturally-occurring Ig, a variant of anaturally-occurring Ig, a recombinant Ig, a chimeric Ig, a humanized Ig.

For instance, the target protein may be selected from the groupconsisting of plasma human fibrinogen, recombinant human fibrinogen,variants of human fibrinogen, fragments of human fibrinogen, plasmahuman IgG, recombinant human IgG, chimeric IgG, humanized IgG, variantsof human IgG, Fc fragment from human IgG and Fc variants from human IgG.

Step (a) comprises contacting the protein target with a candidatemixture of nucleic acids at a pH promoting the formation of positivecharges on the histidine-containing surface domain of said proteintarget.

The candidate mixture of nucleic acids is generally a mixture ofchemically synthesized random nucleic acid. The candidate mixture maycomprise from 10⁸ to 10¹⁸, typically about 10¹⁵ nucleic acids. Thecandidate mixture may be a mixture of DNA nucleic acids or a mixture ofRNA nucleic acids. In some embodiments, the candidate mixture consistsof a multitude of single-stranded DNAs (ssDNA), wherein each ssDNAcomprises a central random sequence of about 20 to 100 nucleotidesflanked by specific sequences of about 15 to 40 nucleotides whichfunction as primers for PCR amplification. In some other embodiments,the candidate mixture consists of a multitude of RNA nucleic acids,wherein each RNA comprises a central random sequence of about 20 to 100nucleotides flanked by primer sequences of about 15 to 40 nucleotidesfor RT-PCR amplification. In some embodiments, the candidate mixture ofnucleic acids consists of unmodified nucleic acids, this means that thenucleic acids comprise naturally-occurring nucleotides only. In someother embodiments, the candidate mixture may comprisechemically-modified nucleic acids. In other words, the nucleic acids maycomprise one or several chemically-modified nucleotides. The chemicalmodification(s) can be performed in order to improve the stability ofthe nucleic acids, for instance to nucleases. In RNAs, the ribose 2′-OHgroup of pyrimidine may be replaced with a 2′-NH2, 2′-F, or a 2′-OMe.Chemical modifications can be also introduced on the C-5 position ofpyrimidines or at C-8 position of purines. Alternatively, modificationsin the phosphate backbone of nucleic acids can be introduced byreplacing a phosphodiester linkage by phosphorothioate linkage. Othermodifications can be introduced for quantification purpose during theSELEX process such as the incorporation of radioactive labellednucleotides or the attachment of fluorescent molecule to the 5′-end ofthe nucleic acids.

In some embodiments, the candidate mixture of nucleic acids is devoid ofany 5-modified deoxyuridine-containing nucleic acids. In some otherembodiments, the candidate mixture is devoid of any 5-modifiedpyrimidine-containing nucleic acids and/or any boronic acid-modifiednucleotides. In some further or additional embodiments, the candidatemixture of nucleic acids is devoid of any nucleic acids comprisingchemically-modified nucleotides. In other words, the candidate mixtureof nucleic acids consists of nucleic acids comprisingnaturally-occurring nucleotides only. In some other embodiments, thecandidate mixture comprises nucleic acids having a chemically-modifiednucleotide at their 5′-end and/or 3′-end only. In preferred embodiments,the candidate mixture consists of single-stranded DNAs.

In step (a), the target protein and the candidate mixture are contactedin pH conditions enabling positive charges to be formed on at least oneof the histidine-containing surface domains of the target protein. Inparticular, the pH of step (a) may be selected so as to promote theprotonation of the histidine residue(s) present in ahistidine-containing surface domain

Indeed, the pKa of histidine in free-state is 6.0. However, the pKa ofthe histidine in protein structure may vary depending on the amino acidspresent in its vicinity. The pH of step (a) is generally below than 7.0and preferably around pH 6.0.

The pH to implement step (a) depends on the protein target of interest,but is typically selected from pH 4.0 to 6.9, preferably from 5.0 to 6.9such as a pH of 5.3 to pH 6.7. A pH of 5.3 to pH 6.7 encompasses a pH of5.3 to 5.5, a pH of 5.5 to 5.7, a pH of 5.7 to 5.9, a pH of 5.9 to 6.1,a pH of 6.1 to 6.3, a pH of 6.3 to 6.5, and a pH of 6.5 to 6.7. Forinstance, if the protein target is human fibrinogen, step (a) may beperformed at a pH of 6.2 to 6.6, for instance of about 6.3.

As another example, if the target protein is a human immunoglobulin of Gisotype or human Fc fragment thereof, step (a) may be performed at a pHof 5.0 to 6.0, for instance 5.5.

Typically, the pH of step (a) may be selected so that the electrostaticsurface potential of the histidine-containing surface domain ispositive.

The skilled artisan may determine the appropriate pH to use in step (a)by molecular modelling, in particular by determining the surface chargedistribution. Typically, the pH of step (a) can be determined bygenerating the surface electrostatic potential maps of the protein atdifferent pHs. The surface electrostatic potential maps of the proteintarget may be obtained by a software which calculates the electrostaticsurface potential from crystal structures or homology models. Forinstance, one may use PDB2PQR software (Dolinsky et al. . Nucleic AcidsResearch 32 W665-W667 (2004) or Pymol software equipped with APBS plugin(Baker et al., Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001).

Accordingly, in some embodiments of the invention, the pH used in stepa) is identified by surface electrostatic potential mapping at differentpHs.

It goes without saying that the pH for step (a) is also selected in viewof the pH stability of the target protein. Typically, the pH of step (a)is selected in the pH range wherein the protein target is stable. Thus,the pH of step (a) may be selected so as to promote a positiveelectrostatic surface potential on the histidine-containing surfacedomain while being in the pH stability range for the target protein. Forinstance, the pH of step (a) may be selected so as to be included in thepH stability range of the target protein and sufficiently distant fromthe upper and the lower limits of the range, typically by a ΔpH of atleast 0.1, such as a ΔpH of at least 0.2, 0.3, 0.4 or 0.5.

In other words, the pH of step (a) may be determined as a pH valueincluded in the pH stability range of the protein target and whichenables to promote a positive electrostatic surface potential on atleast one histidine-containing surface domain of said protein target.

In step (a), the target protein and the candidate mixture are contactedat the desired pH and in conditions enabling the formation of complexbetween the protein target and nucleic acids displaying affinity forsaid protein target. Such conditions favourable for the binding of theprotein target to nucleic acids having affinity to said targets compriseappropriate conditions of temperature, ionic strength and period ofincubation. The candidate mixture is incubated with the protein targetfor a period of time sufficient to enabling the formation of thecomplexes. Typically, the incubation may last several minutes to severalhours, for instance from 10 minutes to 2 hours. A complex corresponds tothe binding of a nucleic acid to a molecule target, i.e. to nucleicacid-protein target pair.

Step (a) may be performed in a buffered aqueous solution. The bufferingagent may be selected from any buffer agents enabling to obtain thedesired pH and compatible with the protein targets and the nucleic acidsmixture.

The buffer agent may be selected from, without being limited to,3-(N-morpholino)propanesulfonic acid (MOPS),2-(N-morpholino)ethanesulfonic acid (MES), HEPES, Bis-TRIS, citrate andacetate. The buffering agent may be present at a concentration of about5 mM to 1 M, for instance from 10 mM to 500 mM, for instance from 10 mMto 200 mM such as about 50 mM.

In some embodiments, the protein target may be present in free-state instep (a). In some other embodiments, the protein target may beimmobilized on a solid support in order to make easier the subsequentseparation of the complex formed by the protein target with certainnucleic acids and the unbound nucleic acids in step (b). For instance,the protein target may be immobilized onto magnetic beads, on solidsupport for chromatography such as sepharose or agarose, on microplatewells and the like. Alternatively, the protein target may be tagged withmolecules useful for capturing of the complex in step (b). For instance,the protein target may be biotinylated.

Step (b) aims at recovering nucleic acids which bind to the proteintarget in step (a), while removing unbound nucleic acids. Typically,step (b) comprises separating the complex formed in step (a) fromunbound nucleic acids, and then releasing the nucleic acids from thecomplex whereby a new mixture of nucleic acids with increased affinityto the target protein is obtained. The separation of the complex fromthe unbound nucleic acids may be performed by various methods and maydepend on the features of the protein target. These methods includewithout being limited to, affinity chromatography, capillaryelectrophoresis, flow cytometry, electrophoretic mobility shift, SurfacePlasmon resonance (SPR), centrifugation, ultrafiltration and the like.The skilled artisan may refer to any separation methods described in thestate in the art for SELEX processes, and for instance described inStoltenburg et al. Biomolecular Engineering, 2007, 24, 381-403, thedisclosure of which being incorporating herein by reference. Asillustration only, if the protein target is immobilized on a support,the separation may be performed by recovering the support, washing thesupport with an appropriate solution and then releasing nucleic acidsfrom the complex immobilized on the support. If the protein target hasbeen incubated in free-state with the candidate mixture, the separationof the nucleic acid-protein complex from unbound nucleic acids can beperformed by chromatography by using a stationary support able tospecifically bind to the protein target or the possible tag introducedon the protein target, whereby the complexes are retained on the supportand the unbound nucleic acids flow out. For instance, one may use astationary phase having thereon antibodies directed against the targetprotein. Alternatively, the partitioning may be performed byultrafiltration on nitrocellulose filters with appropriate molecularweight cut-offs. Once the complexes separated from unbound nucleicacids, the nucleic acids which bind to the protein target are releasedfrom the complexes. The release can be performed by denaturingtreatments such as heat treatment or by elution.

The dissociation between the protein target and the bound nucleic acidsmay be performed by increasing the ionic strength or by modulating thepH in the buffer used in step b) as compared to the buffered solutionused in step a).

Preferably, the dissociation is obtained by increasing the pH in step b)as compared to step a). In the present case, the pH used in step b) maybe higher than the pH used in step (a) of a ΔpH of at least 0.3,preferably of at least 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4,or 1.5. In particular, the pH may be included in the pH range defined by[pH_(step(a))+0.5; pH_(step(a))+1.5 ]. For instance, if the pH of step(a) is 6.4, the pH of the elution buffer may be from 6.9 to 7.9, such as7.4.

Typically, in step b) a pH of more than 7.0, in particular a pH from 7.0to 8.0 such as 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0 maybe used to dissociate the complex and thus recover the nucleic acidsbinding to the protein target.

In alternate or additional embodiments, the elution buffer may compriseEDTA or detergent such as SDS, or urea. For instance, the elution buffermay comprise EDTA at a concentration of about 100 mM to 500 mM. In someother embodiments, the elution buffer is devoid of EDTA and/or anydetergent.

In a preferred embodiment, in step b), the step of releasing the nucleicacids from the complex comprises a step of dissociating the complex byincreasing the pH at a value higher than that used in step a) of a ΔpHof at least 0.8 such as 1.0. Typically, the elution buffer in step b)may have a pH above 7.0, preferably from 7.0-8.0 e.g. 7.2 to 7.8, forinstance 7.3, 7.4, 7.5, 7.6 or 7.7. Preferably, the complex isimmobilized on a solid support by the mean of the protein target. Thismeans that the protein target is immobilized by covalent or non-covalentinteractions on the solid support as described above. After an optionalwashing step, typically with the buffer used in step a), the complexbetween the bound nucleic acids and the protein target can bedissociated with an elution buffer having a pH of at least 7.0,typically from 7.0 to 8.0. The nucleic acids are thus recovered in theelution buffer. In some embodiments, such step is performed bychromatography.

Without to be bound by any theory, the Applicant believes that usingsuch mild conditions of dissociation in step b) may enable to selectaptamers with appropriate binding properties for use in purification. Inparticular, the switch of pH between step (a) and step (b) can addselectivity, whereby aptamers binding to the protein target in apH-dependent manner can be identified.

In step (c), the nucleic acids recovered in step (b) are amplified so asto generate a new mixture of nucleic acids. This new mixture ischaracterized by an increased affinity to the target protein as comparedto the starting candidate mixture.

The amplification may be performed by any method enabling to increasethe amount or the number of nucleic acid copies. For RNAs, theamplification is typically performed by reverse transcription PCR(RT-PCR). In the case of DNAs, the amplification is performed by PCR(Polymerase Chain Reaction), which leads to double-stranded DNAs. Thedouble-stranded DNAs are then separated into single-stranded DNAs so asto obtain a new mixture of single-stranded DNAs. The separation of the“wanted” strands from their “complementary unwanted strands” can beperformed by various methods described in the state in the art.

For instance, one can use the streptavidin/biotin system. A biotinmolecule can be added onto the unwanted strand during the amplification.The double-stranded DNAs may be then immobilized on streptavidin-coatedsurface and the wanted single-stranded DNAs can be recovered after DNAdenaturation while the unwanted strands remain immobilized onto thesurface. Other possibilities is to perform asymmetric PCR in whichspecific primers are used to create a size difference between the“wanted strands” and the “unwanted strands” whereby they can beseparated for instance by subsequent electrophoresis.

Step (a), (b) and (c) form together a round of selection. As indicatedin step (d), this round of selection can be repeated several times,typically 6-20 times until obtaining an aptamer or a pool of aptamersdirected against the target protein. It goes without saying that thestep (a) of round “N” is performed with the mixture of nucleic acidsobtained in step (c) of the round “N−1”. At the end of each selectionround, the complexity of the mixture obtained in step (c) is reduced andthe enrichment in nucleic acids which specifically bind to the targetprotein is increased.

The conditions for implementing step (a), (b) and (c) may be the same ormay be different from one round of selection to another. In particular,the conditions of step (a) (e.g. the incubation conditions of the targetprotein with the mixture of nucleic acids) can change. For instance,step (a) of round “N” can be performed in more drastic conditions thanin round “N+1” in order to direct the selection to aptamers having thehighest affinity for the protein target. Typically, such result can beobtained by increasing the ionic strength of the buffer used in step(a).

The method of the invention may comprise one or several additionalsteps.

In particular, the process may comprise a step, prior to step (a), ofdetermining the pH for implementing step (a).

The pH to be used in step (a) may be determined by molecular modellingas described above.

In some embodiments, such step comprises modelling the surfaceelectrostatic maps of the protein at different pHs and selecting a pHfor implementing step a) which enables to create a positive surfaceelectrostatic potential on the histidine-containing surface domain andwhich belongs to the pH stability range of the protein.

The method of the invention may comprise counter-selection orsubtractive selection rounds. The counter-selection rounds may aim ateliminating nucleic acids which cross-react with other entities ordirecting the selection to aptamers binding to a specific domain of theprotein target. The additional counter-selection round(s) depend on thecontemplated use of the final aptamers. If the aptamer is to be used asaffinity ligand for the purification of a transgenic human proteinexpressed in a transgenic animal naturally expressing a proteinhomologous to said human protein, the method of the invention maycomprise a step of removing aptamers which binds to said homologousprotein. Thus, the method may comprise one or several rounds ofselection wherein aptamers binding to a protein homologous to theprotein target are removed.

Alternatively, the method of the invention may comprise additionalround(s) of selection in order to identify aptamers able to bind to thetarget protein regardless its glycosylation state.

For illustration, the first selection rounds can be performed with anon-recombinant protein target, and the subsequent selection rounds canbe performed with a recombinant protein target produced in transgenicanimal or in host cell such as bacterium or yeast. As an example, inorder to identify aptamers capable of specifically binding to humanfibrinogen from human plasma and to human fibrinogen produced intransgenic animal, certain rounds of selection may be performed withhuman plasma fibrinogen as protein target and the remaining rounds ofselection may be performed with transgenic human fibrinogen as proteintarget.

The method of the invention may also comprise one or several additionalsteps following the generation of the final pool of aptamers.

The method of the invention may comprise one or several of the followingsteps:

-   -   a step of cloning the aptamer pool,    -   a step of sequencing an aptamer,    -   a step of producing an aptamer, for instance by chemical        synthesis,    -   a step of identifying consensus sequences in the pool of        aptamers, for instance by sequence alignment,    -   a step of optimizing the sequence of an aptamer,

In some embodiments, the method of the invention may comprise thefollowing additional steps:

-   -   sequencing an aptamer obtained in step (c)    -   optimizing said aptamer, and    -   producing the optimized aptamer, preferably by chemical        synthesis.

The optimization of the aptamer may comprise the determination of thecore sequence of the aptamer, i.e. the determination of the minimalnucleotide moiety able to specifically bind to the protein target.Typically, truncated versions of the aptamer are prepared so as todetermine the regions which are not important in the direct interactionwith the protein target.

The binding capacity of the starting aptamer and the truncated versionsmay be assessed by any appropriate methods such as SPR.

Alternatively or additionally, the sequence of the aptamer may besubjected to mutagenesis in order to obtain aptamer mutants, forinstance with improved affinity or specificity as compared to theirparent aptamer. Typically one or several nucleotide modifications areintroduced in the sequence of the aptamer. Nucleotide modificationsinclude the deletion of a nucleotide, the insertion of a nucleotide orthe replacement of a nucleotide by another nucleotide. The resultingmutants are then tested for their ability to specifically bind to theprotein target, for example by SPR or ELISA-type assay.

In additional or alternate embodiments, the optimization may compriseintroducing one or several chemical modifications in the aptamer.Typically, such modifications encompass replacing nucleotide(s) of theaptamer by corresponding chemically-modified nucleotides. Themodifications may be performed in order to increase the stability of theaptamers or to introduce chemical moiety enabling functionalization orimmobilization on a support. Appropriate chemical modifications arethose detailed above and encompass 2′-ribose modifications such 2′-F,2′-NH2, and 2′-OMe, phosphorothiate replacement of phosphodiester groupand the likes. Caps such as amine, phosphate, PEG, cholesterol fattyacids and the like may be introduced at the 3′ and/or 5′-end of theaptamer. At last, the chemical modifications may encompass theintroduction of labels or tags such as biotin, fluorescent molecules,dyes, and the like at the 3′ and/or 5′ end of the aptamer.

Particular Embodiments of the Method of the Invention

In a particular aspect, the invention relates to a method for obtainingan aptamer against fibrinogen, said method comprising:

-   -   a) contacting fibrinogen with a candidate mixture of nucleic        acids at a pH lower than 7.0, preferably from 5.8 to 6.8,    -   b) recovering nucleic acids which bind to fibrinogen, while        removing unbound nucleic acids,    -   c) amplifying the nucleic acids obtained in step (b) to yield to        a candidate mixture of nucleic acids with increased affinity to        fibrinogen, and    -   d) repeating steps (a), (b), (c) until obtaining one or several        aptamers against fibrinogen.

Step a) is performed in conditions favourable for the binding offibrinogen with nucleic acids having affinity for said fibrinogen.Preferably, the pH of step a) is from 6.0 to 6.6, such as 6.1, 6.2, 6.3,6.4 and 6.5.

An appropriate pH for step a) is for instance, 6.3±0.1. Such pH enablesto protonate at least one surface histidine of fibrinogen.

Preferably, fibrinogen is a human fibrinogen or a variant thereof.Fibrinogen may be a plasma human fibrinogen or a transgenic humanfibrinogen, as explained in section entitled “Method for obtaining anaptamer against a protein target comprising a histidine-containingsurface domain”.

Step b) typically comprises the steps of separating the complex formedin step (a) from unbound nucleic acids, and then releasing the boundnucleic acids from the complex. The dissociation of the complex betweenfibrinogen and bound nucleic acids can be performed by increasing the pHabove 7.0 in step b). Typically, in step b) the nucleic acids arerecovered by dissociating the complex between fibrinogen and the nucleicacids at a pH above 7.0, for instance from pH 7.0 to 8.0, preferablyfrom pH 7.2 to 7.8, more preferably from 7.2 to 7.6, such as 7.4.

In preferred embodiments, in step b), the complex is immobilized on asolid support by the mean of the protein target. This means that theprotein target is immobilized by covalent or non-covalent interactionson the solid support as described above. After an optional washing step,typically with the buffer used in step a), the complex between thenucleic acids and the protein target can be dissociated with an elutionbuffer having a pH from pH 7.0 to 8.0, preferably from pH 7.2 to 7.8,more preferably from 7.2 to 7.6, such as 7.4. The nucleic acids are thusrecovered in the elution buffer.

In another particular aspect, the invention relates to a method forobtaining an aptamer against a target protein selected from aFc-containing protein, or a Fc fragment, said method comprising:

-   -   a) contacting the target protein with a candidate mixture of        nucleic acids at a pH lower than 7.0, preferably from 5.0 to        6.0,    -   b) recovering nucleic acids which bind to the protein target,        while removing unbound nucleic acids,    -   c) amplifying the nucleic acids obtained in step (b) to yield to        a candidate mixture of nucleic acids with increased affinity to        the protein target, and    -   d) repeating steps (a), (b), (c) until obtaining one or several        aptamers against the protein target.

Step a) is performed in conditions favourable for the binding of thetarget protein with nucleic acids having affinity for said fibrinogen.

Preferably, the pH of step a) is from 5.2 to 5.8, such as 5.3, 5.4, 5.5,5.6, and 5.7. An appropriate pH for step a) is for instance 5.5±0.1.

Preferred Fc-containing proteins are immunoglobulins as defined in theabove section, preferably human immunoglobulins from human plasma orrecombinantly produced.

Step b) typically comprises the steps of separating the complex formedin step (a) from unbound nucleic acids, and then releasing the nucleicacids from the complex. The dissociation of the complex between theprotein target and the bound nucleic acids can be performed byincreasing the pH above 6.0 in step b). Typically, in step b) thenucleic acids are recovered by dissociating the complex at a pH above7.0, for instance from pH 7.0 to 8.0, preferably from pH 7.2 to 7.8,more preferably from 7.2 to 7.6, such as 7.4.

In preferred embodiments, in step b), the complex is immobilized on asolid support by the mean of the protein target. This means that theprotein target is immobilized by covalent or non-covalent interactionson the solid support as described above. After an optional washing step,typically with the buffer used in step a), the complex between thenucleic acids and the protein target can be dissociated with an elutionbuffer having a pH from pH 7.0 to 8.0, preferably from pH 7.2 to 7.8,more preferably from 7.2 to 7.6, such as 7.4. The nucleic acids are thusrecovered in the elution buffer.

It goes without saying that the conditions to implement steps a), b), c)and d) in the two above methods may be as defined in the sectionentitled “Method for obtaining an aptamer against a protein targetcomprising a histidine-containing surface domain”.

Method for Obtaining an Aptamer Against Any Protein Target

In another aspect, the invention relates to a method for obtaining anaptamer against a protein target, which comprises:

-   -   (i) determining a pH value promoting positive charges in at        least one surface domain of the protein target,    -   a. contacting the protein target with a candidate mixture of        nucleic acids at the pH determined in step (i) in conditions        favourable for binding of the protein target with nucleic acids        having affinity for said targets,    -   b. recovering nucleic acids which bind to the protein target,        while removing unbound nucleic acids,    -   c. amplifying the nucleic acids obtained in step (b) to yield to        a candidate mixture of nucleic acids with increased affinity to        the protein target,    -   d. repeating steps (a), (b), (c) until obtaining one or several        aptamers against the protein target of interest.

The conditions to implement steps a), b), c) and d) may be as definedabove in the section entitled “Method for obtaining an aptamer against aprotein target comprising a histidine-containing surface domain” exceptfor the condition of pH in step (a) which is determined as stated instep (i).

The protein target may be any protein target of interest. In particular,the protein target may be selected among the group consisting ofantibody, antigen, growth factor, receptor, enzyme, glycoprotein, afragment or variant thereof. In certain embodiments, the protein targetis a plasma protein such as immunoglobulin and fibrinogen.

Step (i) can be typically performed by molecular modelling by usingsoftware such as Modeller. In some embodiments, the molecular modellingmay be based on data obtained from crystalline structure of the protein.In other embodiments, the molecular modelling may be performed from theprimary sequence of the protein by comparison with homologous proteinsfor which the three-dimensional structure is known.

Preferably, the pH determined in step (i) enables to create a positivesurface electrostatic potential in at least one surface domain of theprotein target. Typically, step (i) may comprise the modelling of theelectrostatic potential maps for the protein target at different pHs byusing modelling software such as Modeller. The pH of interest isselected among the pH(s) enabling to generate a positive surfaceelectrostatic potential on at least one surface domain of the protein,in view of the pH stability range of the protein. In other words, the pHin step (i) is selected in the overlap of the pH stability range of thetarget protein and the pH range enabling the presence of a positivesurface electrostatic potential on a surface domain of the proteintarget.

In some embodiments, step (i) may comprise the steps of:

-   -   determining the presence of a histidine-containing surface        domain in the protein target, and    -   if said domain is present, determining a pH promoting positive        charges, preferably enabling to obtain a local positive        electrostatic potential, in said histidine-containing surface        domain.

As mentioned above, for a given protein, the presence of “ahistidine-containing surface domain” can be determined by molecularmodelling from the primary sequence of the protein. For instance, thetertiary or quaternary structure of the protein can be predicted fromthe primary amino acid sequence by using modelling software such asModeller by comparison with homologous proteins. The presence of “ahistidine-containing surface domain” can also be determined from thecrystalline structure of the protein.

It goes without saying that said method may comprise one or severaladditional steps such as those listed for the “Method for obtaining anaptamer against a protein target comprising a histidine-containingsurface domain”. In particular, said method may comprise one or severalof the following steps:

-   -   a step of counter-selection    -   a step of cloning the aptamer pool,    -   a step of sequencing an aptamer,    -   a step of producing an aptamer, for instance by chemical        synthesis,    -   a step of identifying consensus sequences in the pool of        aptamers, for instance by sequence alignment, and    -   a step of optimizing the sequence of an aptamer,

Aptamers of the Invention and Uses Thereof

Without to be bound by any theory, the Applicant is of the opinion thatthe methods of the invention enable to obtain aptamers which differ fromthe aptamers described in the prior art in virtue of their uniquebinding properties. In particular, said aptamers specifically bind tothe protein of interest as defined above with a high affinity. Thedissociation constant (Kd) of said aptamer for their target molecule istypically from 10⁻¹² to 10⁻⁶ M, preferably from 10⁻¹² to 10⁻⁸ M.Noteworthy, the aptamers obtained by the method of the invention maybind to their protein target in a pH-dependent manner. As illustrated inthe example, the anti-fibrinogen aptamers identified by the method ofthe invention specifically bind to fibrinogen at pH 6.3, and not at pH7.4. Similarly, the identified anti-Fc aptamers specifically bind to IgGat pH 5.5 and not at pH 7.4.

As used herein, an aptamer binds to its protein target in a pH-dependentmanner means that the affinity of the aptamer for its protein targetdepends on the pH. In particular, the dissociation constant (Kd) mayvary depending on the pH. In the context of the invention, the aptamermay have a higher affinity at a slightly acid pH as compared tophysiological pH. In other words the Kd of the aptamer may be at least2-fold higher, in particular, at least 5, 10, 20, 50, 100, 500, or1000-fold at physiological pH than at slightly acid pH. Typically aphysiological pH is a pH of about 7.0-7.8, preferably from 7.0 to 7.7such as 7.0-7.5, in particular 7.2, 7.3 or 7.4.

A slightly acid pH is typically a pH from 4.5 to 6.9, such as 5.0 to6.8. For instance, a slightly acid pH may be from 5.3 to 5.7, e.g. 5.5,if the protein target is an immunoglobulin or a Fc fragment. A slightlyacid pH may be from 6.0 to 6.5, e.g. 6.3 or 6.4, if the protein targetis a fibrinogen.

In some preferred embodiments, the aptamers of the invention does notbind to its protein target at a pH higher than 7.0.

Moreover, as illustrated in the Examples, the aptamers identified by themethod of the invention can be used as affinity ligands in thepurification of the protein target, because the complex formed by saidaptamers and their protein target can be dissociated in mild conditionsof elution. Noteworthy, said aptamers may be used for the purificationof the protein target from very complex media such as body fluids,including blood, plasma, milk and derivatives thereof.

Accordingly, a further object of the invention is an aptamer obtainableor obtained by the methods of the invention.

In a specific aspect, the invention relates to an aptamer whichspecifically binds to a protein target comprising a histidine-containingsurface domain. Said protein target may be as defined above. Inparticular, such protein target may be selected among proteinscomprising a histidine-containing domain and having at least one of thefollowing features:

-   -   The protein target has an isoelectric point (pI) of less than        7.5, preferably less than 7.0 such as a pI of 4.0 to 6.9.    -   The protein target is devoid of any surface domain with positive        electrostatic potential at pH of more than 7.0.

In some embodiments, the protein target is selected from the groupconsisting of fibrinogen, immunoglobulins and fragments or variantsthereof as well as any Fc-containing proteins such as Fc-fusionproteins. For instance, the target protein may be selected from thegroup consisting of plasma human fibrinogen, recombinant humanfibrinogen, variants of fibrinogen, fragments of fibrinogen, plasmahuman IgG, recombinant human IgG, chimeric IgG, humanized IgG, variantsof human IgG, Fc fragment from human IgG and Fc variants from human IgG.

The aptamer of the invention may be a deoxyribonucleic acid (DNA) or aribonucleic acid (RNA). Preferably, the aptamer is a DNA aptamer. Theaptamer may comprise one or several chemically-modified nucleotides asdetailed herein. In certain embodiments, the aptamer may comprise amodified nucleotide at its 3′-end or/and 5′-end only (i.e. the firstnucleotide and/or the last nucleotide of the aptamer is/are the solechemically-modified nucleotide(s)). Preferably, said modified nucleotidemay enable the grafting of the aptamer onto a solid support, or thecoupling of said aptamer with any moiety of interest (e.g. useful fordetection or immobilization). In some embodiments, the aptamer of theinvention is devoid of any 5-modified deoxyuridine or boronicacid-modified nucleotides. In some other embodiments, the aptamer of theinvention is devoid of any chemically-modified nucleotides.

As mentioned above, the affinity of the aptamer to its protein targetmay be pH-dependent. In a particular embodiment, the invention relatesto an aptamer directed against fibrinogen, said aptamer being able tobind fibrinogen at a pH lower than 6.8, preferably at a pH lower than6.8 and higher than 6.0, for instance 6.2-6.6, such as 6.4, withoutbinding to fibrinogen at a pH higher than 7.0 such as 7.4.

In another embodiment, the invention relates to an aptamer directedagainst Fc fragment from a human IgG, said aptamer being able to bindsaid Fc fragment at a pH lower than 6.0, preferably at a pH lower than6.0 and higher than 5.0, for instance at a pH 5.2-5.7, such as 5.5without binding to Fc fragment at a pH higher than 7.0, preferablyhigher than 6.0.

The aptamers of the invention find applications in several fields, inparticular in the purification and the detection field. In particular,the aptamers of the invention can be used to prepare affinity ligands.

A further object of the invention is thus an affinity ligand comprisingan aptamer of the invention. Typically, the affinity ligand of theinvention comprises (i) an aptamer moiety, i.e. an aptamer as definedabove linked to at least one (ii) non-aptamer entity useful forimmobilization on an appropriate substrate. Preferably, the non-entityaptamer is preferably linked to the 5′- or the 3′-end of the aptamer.

In certain embodiment, the affinity ligand may comprise a mean ofimmobilization linked to the aptamer moiety directly or by a spacergroup. Accordingly, the affinity ligand may comprise, or consist of, acompound of formula (IV):

[IMM]-([SPACER])_(p)-[APTAMER] wherein

-   -   [APTAMER] denotes an aptamer as defined above,    -   [SPACER] is a spacer group,    -   [IMM] is a moiety for the immobilization of the aptamer onto a        support and    -   p is 0 or 1.

p is 0 means that the spacer is absent and that [IMM] is directly linkedto [APTAMER], preferably at the 3′ or the 5′-end of aptamer.

p is 1 means that the spacer is present and links to [IMM] and[APTAMER].

The spacer group is typically selected to decrease the steric hindranceof the aptamer moiety and improve its accessibility while preserving theaptamer capability of specifically binding to its protein target. Thespacer group may be of any type. The spacer may be a non-specificsingle-stranded nucleotide, and may comprise from 2 to 20 nucleotides inlength. Examples of appropriate nucleic spacers are polyA and polyT. Insome other embodiments, the spacer may be a non-nucleic chemical entity.For instance, the spacer may be selected from the group consisting of apeptide, a polypeptide, an oligo- or polysaccharide, a hydrocarbon chainoptionally interrupted by one or several heteroatoms and optionallysubstituted by one or several substituents such as hydroxyl, halogens,or C₁-C₃ alkyl; polymers including homopolymers, copolymers and blockpolymers, and combinations thereof. For instance the spacer may beselected from the group consisting of polyethers such as polyethyleneglycol (PEG) or polypropylene glycol, polyvinylic alcool, polyacrylate,polymethacrylate, polysilicone, and combination thereof. For instance,the spacer may comprise several hydrocarbon chains, oligomers orpolymers linked by any appropriate group, such as a heteroatom,preferably —O— or —S—, —NHC(O)—, —OC(O)—, —NH—, —NH—CO—NH—, —O—CO—NH—,phosphodiester or phosphorothioate. Such spacer chains may comprise from2 to 200 carbon atoms, such as from 5 to 50 carbon atoms or such as 2 to20 atom carbons. Preferably, the spacer is selected from non-specificoligonucleotides, hydrocarbon chains, polyethers, in particularpolyethylene glycol and combinations thereof.

A further object of the invention is an affinity support comprising asolid support having thereon a plurality of aptamers or affinity ligandsas defined above. The solid support may be of any type. For instance,the solid support may be a polymeric gel, filter or membrane. Inparticular, the solid support may be composed of agarose, cross-linkedagarose, cellulose or synthetic polymers such as polyacrylamide,polyethylene, polyamide, polysulfone, and derivatives thereof. Suchsupports may be suitable for the purification of the protein target. Forinstance, the solid support may be a support for chromatography, inparticular for liquid affinity chromatography.

Accordingly, the aptamer, the affinity ligand and the affinity supportmay be used in the purification of the protein target.

Alternatively, the aptamers and the affinity ligands of the inventionmay be used in the diagnostic and detection field. In particular, theaptamers and the affinity ligands of the invention may be useful for thediagnostic or the prognostic of diseases or disorders associated with avariation of the expression of the protein target.

In another aspect, the aptamers of the invention may be also used in thetreatments of disorders involving the protein target.

Further aspects and advantages of the present invention are disclosed inthe following experimental section, which should be regarded asillustrative and not limiting the scope of the present application.

List of sequences SEQ ID NO Sequences Description 1GGGTCAATGCCAGGTCTCGGACCTGGAATCCGCCACCCGC Anti-fibrinogenATTAGAACCAGGGTTGACATCGGCTCGCAAGCAGTC aptamer (aptamer A5-1) 2GGGTCAATGCCAGGTCTCAACTTTCGCGTGTGGTTGGTAGG Anti-fibrinogenGCTAGGTGTATACGCATATCGGCTCGCAAGCAGTC aptamer (aptamer A5-2) 3GGGTCAATGCCAGGTCTCGGACCTGGAATCCGCCACCCGC Anti-fibrinogenATTAGAACCAGGGTTGAC aptamer - core sequence of SEQ ID NO: 1(aptamer A5-1.9) 4 CGCGTGTGGTTGGTAGGGCTAGGTGTATACGCAT Anti-fibrinogenaptamer - core sequence of SEQ ID NO: 2 (aptamer A5-2.9) 5GGGTCAATGCCAGGTCTCCCCAGCCTCATCTCACGGCATAG Anti-Fc aptamerTCTCGCCACACTGGAAATCGGCTCGCAAGCAGTC (aptamer A6-2) 6GGGTCAATGCCAGGTCTCCACGGTATAGTCTCGCCCAGTGC Anti-Fc aptamerCCTTTGTTGGACTTCCTATCGGCTCGCAAGCAGTC (aptamer A6-8)

EXAMPLE 1 Identification of Anti-Fibrinogen Aptamers by the Method ofthe Invention

1. Material and Method

Oligonucleotide Library

The ssDNA library used to perform SELEX process consisted of a 40-baserandom region flanked by two constant 18-base primer regions.

Fibrinogen

The protein target was human fibrinogen. Different sources of humanfibrinogen were used during Selex process:

Human fibrinogen: Two preparations of human fibrinogen were used aspurified composition from human plasma with a purity of 95% and 99.9%,respectively.

Transgenic fibrinogen: Transgenic Fibrinogen was purified from the milkof transgenic cows to 97% purity.

SELEX Protocol

Fibrinogen (97% pure transgenic Fibrinogen for round 1 to 3 and 95% pureplasmatic Fibrinogen for round 4&5 and 99.9% pure plasmatic Fibrinogenfor round 6 to 8) was immobilised on an affinity resin, while the amountof target immobilised on the resin continuously decreased from round 1to 8 (see FIG. 2).

The immobilised target was incubated with the ssDNA library/pool atdecreasing concentrations using as selection buffer (50 mM MOPS pH 6.30,150 mM NaCl, 5 mM MgCl₂) at decreasing incubation time (see table ofFIG. 2).

The fibrinogen/ssDNA containing resin was recovered and washed withselection buffer during round 1 & 2 and wash buffer containing 50 mMMOPS pH 6.30, 500 mM NaCl, 5 mM MgCl₂ from round 3 to 8 (see table ofFIG. 2). After washing, the bound ssDNA was eluted using elution buffer(50 mM Tris-HCl pH 7.40, 200 mM EDTA). Before every round (except thefirst round) a counter selection step was performed by incubating thessDNA pool with the affinity resin in order to prevent the enrichment ofanti-support aptamers. The parameters of the SELEX protocols aredepicted in FIG. 2.

Determination of the Binding Affinity of Aptamers by SPR

The selected aptamer was synthetized with Biotin and a triethyleneglycol spacer at the 5′ end of the oligonucleotide. A 1 μM solution ofthe aptamer was prepared using the SELEX selection buffer. The aptamersolution was heated to 90° C. for 5 min, incubated on ice for 5 min andequilibrated to room temperature for 10 min The preparation was injectedon a streptavidin coated sensor chip SA of Biacore T200 instrument (GEHealthcare) at a flow rate of 10 μl/min for 7 min. Then, differentconcentrations of the target were injected to the immobilised aptamer at30 μl/min for 1 minute. After dissociation for 1-2 min a wash step wasperformed by injecting a suitable wash buffer at 30 μl/min for 1 min.For elution, a suitable elution buffer was injected at 30 μl/min for 1-2min. Finally the sensor chip was regenerated by injection of 50 mM NaOHat 30 μl/min for 30 sec. During the course of the experiment theresponse signal was recorded in a sensorgram.

2. Results

The SELEX method of the invention enables to identify 67 anti-fibrinogenaptamer canditates, among which aptamers of SEQ ID NO:1 and SEQ ID NO:2displayed a high affinity for both plasma and transgenic humanfibrinogen. These aptamers were shown to bind human fibrinogen in a pHdependent manner The core sequences of these aptamers (namely theminimal sequence binding to fibrinogen) were determined. The aptamer ofSEQ ID NO:3 corresponds to the core sequence of aptamer of SEQ ID NO:1.The aptamer of SEQ ID NO:4 is the core sequence of aptamer of SEQ IDNO:2. FIGS. 3A-3D show the binding profile obtained for the coresequences of aptamers of SEQ ID NO:1 and NO:2 by SPR. Aptamers of SEQ IDNO:3 and 4 are able to specifically bind to transgenic fibrinogen andplasma fibrinogen at pH 6.3 in a dose-dependent manner, as evidenced bythe increase of the signals when the concentration of fibrinogen wasincreased. The complex between the aptamers and fibrinogen were notsignificantly dissociated by the increase of NaCl concentration. On theother hands, the injection of a buffer at pH 7.4 enabled to dissociatethe complex between the aptamers and whereby fibrinogen was eluted.

Indeed, the aptamers obtained by the method of the invention bind tofibrinogen in a pH-dependent manner Such a result is illustrated in FIG.4A and 4B for aptamers of SEQ ID NO:3 and SEQ ID NO:4 respectively. Thebinding level of fibrinogen decreased when pH increased. The highestbinding was observed at pH 6.3. The aptamers did not bind to fibrinogenfor pH higher than 6.8.

EXAMPLE 2 Comparative Example

The same SELEX process as in Example 1 was carried out except that theoligonucleotide library was contacted with the purified composition ofplasmatic fibrinogen (95%) for round 1 to 4 and with transgenicFibrinogen from round 5 to 9 using a selection buffer at pH 7.40 and theelution was performed with an aqueous solution comprising 200 mM EDTA atpH 7.40.

The process led to the identification of several aptamers. The bindingproperties of said aptamers were tested by SPR. Each aptamer of interestwas immobilized on the chip of the SPR and then contacted with thepurified composition of fibrinogen. In order to identify the proteinfrom the purified composition which has been bound by the aptamer,several antibodies were tested. Notably, anti-fibrinogen antibodies didnot induce any increase of the signal, showing that the protein capturedby the aptamer was not human fibrinogen. Indeed, the aptamers selectedby the process did not bind to human fibrinogen, but to a contaminantaccounting for less than 1% in the starting purified plasma fibrinogenand not present in the transgenic fibrinogen preparation.

EXAMPLE 3 Preparation of Affinity supports from Aptamers Identified bythe Method of the Invention

1. Material and Method

Affinity Supports

Two affinity supports were prepared by grafting aptamers onNHS-activated Sepharose (GE Healthcare). The first affinity support(affinity support n° 1) was prepared by grafting aptamers of SEQ ID NO:3(aptamer A5-1.9) comprising a C6 spacer with a terminal amino group atits 5′end and an inverted deoxy-thymidine at its 3′ end. The secondaffinity support (affinity support n° 2) was prepared by graftingaptamers of SEQ ID NO:4 (aptamer A5-2.9) comprising comprising a C6spacer with a terminal amino group at its 5′end and an inverteddeoxy-thymidine at its 3′ end.

1 volume of NHS activated Sepharose gel placed in a column was rinsedwith at least 10 volumes of a cold 0.1 M HCl solution, then equilibratedwith at least 8 volumes of cold 100 mM acetate pH 4.0 solution.

After a 3 min-2000 g centrifugation, the supernatant is removed anddrained gel is re-suspended with 2 volumes of aptamer in 100 mM acetatepH 4.0 solution. This suspension is incubated for 2 hours at roomtemperature under stirring.

Then, 1 volume of 200 mM Borate pH 9 is added, this suspension isincubated at room temperature under stirring for 2 h 30.

After a 3 min-2000 g centrifugation, the supernatant is discarded.Drained gel is re-suspended in 2 volumes of Tris-HCl 0.1M pH 8.5solution. Suspension is incubated at +4° C. under stirring overnight.

After incubation, and a 3 min-2000 g centrifugation, the supernatant isdiscarded. The gel is alternatively washed with 2 volumes of Sodiumacetate 0.1M+NaCl 0.5M pH 4.2 and 2 volumes of a Tris-HCl 0.1M pH 8.5solution. This washing cycle is repeated once.

After a 3 min-2000 g centrifugation supernatant is removed. The drainedgel is re-suspended in 2 volumes of equilibration buffer.

EXAMPLE 4 Purification of Fibrinogen from Semi Purified FibrinogenSolution on the Affinity Support of Examples 3

1. Material and Method

Conditions of the Affinity Chromatography

Affinity support n° 1: Thawed semi purified fibrinogen solution (IP1:Fibrinogen Intermediate Product 1) obtained from human plasma wasdiluted 10 times in the binding buffer and was pH adjusted to 6.3.Diluted IP1 was subjected to a chromatography steps on support n° 1.This step was repeated once to obtain enough fibrinogen quantity forultrafiltration step.

Affinity support n° 2: Thawed semi purified fibrinogen solution (IP1:Fibrinogen intermediate product 1) obtained from human plasma wasdiluted 10 times in the binding buffer and pH was adjusted to 6.3.Diluted IP1 was subjected to a chromatography steps on support n° 2.This step was repeated once to obtain enough fibrinogen quantity forultrafiltration step.

The conditions of the affinity chromatography are summarized for eachaffinity support:

Affinity support no1 Affinity support no2 grafted with aptamer graftedwith aptamer moieties of SEQ ID NO: 3 moieties of SEQ ID NO: 4 (A5-1.9)(A5-2.9) Binding MOPS 50 mM, MgCl₂ MOPS 50 mM, NaCl 150 mM, buffer 5 mM,NaCl 150 mM, pH pH 6.3 6.3 Washing None MOPS 50 mM, NaCl 2M, buffer pH7.4 Elution MOPS 50 mM, NaCl MOPS 50 mM, MgCl₂ 2M, buffer 150 mM, pH 7.4pH 7.4

For each affinity support, fibrinogen was eluted in mild conditions bymodification of the buffer composition.

For both chromatography on Affinity support n° 1 and n° 2: 2 eluatefractions were generated and pooled for ultrafiltration step.

Conditions of the Ultrafiltration

For each affinity support, pool of eluate fractions were subjected to anultrafiltration 100 kDa in order to concentrate Fibrinogen and toformulate in sodium citrate 10 mM, arginine 20 g/L at pH 7.4.

Analytical Methods

Proteins Titration methods Fibronectin, antigenic FibrinogenNephelometry Factor II, Factor XI, Factor XIII, Plasminogen ElisaFibrinogen clotting activity Coagulation assay (von Clauss method)

2. Results

The results are shown in FIGS. 7A-7B and 7C-7D. FIGS. 7A and 7B show thechromatography profile obtained for the fibrinogen purification fromsemi purified fibrinogen solution on the affinity support n° 1 and n° 2respectively. Fibrinogen was eluted by increasing the pH to 7.4 and byadding MgCl₂ for affinity support n° 2 and by suppressing Mg²⁺ foraffinity support n° 1. The electrophoresis analysis of the fractionsobtained by chromatography (FIGS. 7C and 7D) showed that contaminantspresent in the loaded material (IP1) are drastically removed with almostonly Fibrinogen visible in the eluate. Additionally, electrophoresisanalysis in reducing conditions shows that Fibrinogen in the eluate isin a native form with no visible degradation (Aα1 is the most importantband of Aα bands)

Yields and fibrinogen concentration obtained are summarized in the tablebelow:

Affinity Affinity support no1 support no2 Chromatography yield (%) 51 71Concentration of antigenic fibrinogen 13.1 14.2 obtained afterultrafiltration (mg/ml)

Active Fibrinogen is demonstrated by a ratio between coagulantFibrinogen and antigenic Fibrinogen close to 1. Analysis on the startingmaterial and the resulting purified fibrinogen prepared with bothaffinity supports are detailed in the following table:

clotting activity Fibrinogen/ratio Fibrinogen g/L clotting/antigenicStarting material 17.6 1.17 (IP1 fibrinogen) Purified Fibrinogen 13.91.06 concentrate - Support no1 Purified Fibrinogen 14.5 1.02concentrate - Support no2

For both purified Fibrinogen, the ratio between clotting and antigenicfibrinogen was about 1.0 for both aptamers. The soft chromatographyconditions allowed the preparation of a purified fibrinogen withpreserved activity.

The table hereunder shows the contaminant proteins titration in thestarting material and the purified fibrinogen fractions:

semi purified Fibrinogen Fibrinogen purified with Fibrinogen purifiedwith Contaminant (starting composition) affinity support no1 affinitysupport no2 proteins Concentration Concentration Removal ConcentrationRemoval Fibronectin 0.55 g/L 0.02 g/L 96.3% 0.02 g/L 95.1% Factor II0.13 mUI/mL 0.03 mUI/mL 70.8% 0.04 mUI/mL 66.3% Factor XI 21.0 mUI/mL2.8 mUI/mL 83.8% 3.6 mUI/mL 80.8% Factor XIII 10000 mUI/mL 10 mUI/mL99.9% 42 mUI/mL 99.5% Plasminogen 56 μg/mL 0.21 μg/mL 99.5% 0.21 μg/mL99.6%

A good elimination of contaminants proteins is obtained with a removalfrom 65% to over than 99% as compared to the starting material.

Chromatography conditions allowed the removal of more than 99.5% ofinitial plasminogen, which is one of the most problematic contaminantwith regards to Fibrinogen stability.

The aptamers identified by the SELEX of the invention are suitable foruse as affinity ligand in the purification of fibrinogen bychromatography. Noteworthy, the aptamers identified by the process ofthe invention enables the selective binding and then the elution offibrinogen in mild and non-denaturing conditions, while removing most ofthe possible contaminants.

EXAMPLE 5 Purification of Fibrinogen by Chromatography from Plasma

Purification on affinity support n° 1: The Plasma was thawed, filtrated0.45 μm, diluted 10 times in the binding buffer and then pH adjusted to6.3. Diluted solution was subjected to a chromatography steps on supportn° 1.

Purification on affinity support n° 2: The Plasma was thawed, filtrated0.45 μm, diluted 10 times in the binding buffer and then pH adjusted to6.3. Diluted solution was subjected to a chromatography steps on supportn° 2.

The conditions of the affinity are summarized, for each affinitysupport, in the table below:

Affinity support no1 Affinity support no2 grafted with aptamer graftedwith aptamer moieties of SEQ ID NO: 66 moieties of SEQ ID NO: 67(A5-1.9) (A5-2.9) Binding buffer MOPS 50 mM, MgCl₂ MOPS 50 mM, NaCl 1505 mM, NaCl 150 mM, mM, pH 6.3 pH 6.3 Washing buffer return to baselinewith MOPS 50 mM, NaCl 2M, the binding buffer pH 7.4 Elution buffer MOPS50 mM, NaCl MOPS 50 mM, MgCl₂ 150 mM, pH 7.4 2M, pH 7.4 RegenerationMOPS 50 mM, MgCl₂ same as the elution buffer buffer 2M, pH 7.4

For each affinity support, fibrinogen was eluted in mild conditions bymodification of the buffer composition. 2. Results

The results are shown in FIGS. 5A-5B and 6A-6B. FIGS. 5A and 6A show thechromatography profile obtained for the purification of fibrinogen fromplasma on the affinity support n° 1 and n° 2 respectively. Noteworthy,most of the contaminant proteins were not retained on the stationaryphase whereas fibrinogen bound to the support. Fibrinogen was eluted byincreasing the pH to 7.4 and by adding 2 M MgCl₂ for affinity support n°2 and by suppressing Mg²⁺ for affinity support n° 1. The electrophoresisanalysis of the fractions obtained by chromatography (FIG. 5B and FIG.6B) showed that fibrinogen was mostly present in the elution fractionwhereas contaminant proteins were present in the non-retained fraction,in the washing fraction or the regeneration fraction. Indeed, theelution fractions migrated as single band. The relative purity(determined by SDS PAGE) of the eluate fibrinogen fractions was greaterthan 95%. Such results demonstrate that the aptamers of the inventionare particularly suitable for a use as affinity ligands in thepurification of fibrinogen from complex starting compositions.

EXAMPLE 6 Identification of Anti-IgG Aptamers by the Method of theInvention

1. Material and Method

Oligonucleotide Library

The ssDNA library used in the SELEX process of the invention consistedof a 40-base random region flanked by two constant 18-base primerregions.

Human Polyclonal IgG-Fc Fragments

The protein target used for the SELEX was highly pure human polyclonalIgG, Fc fragment. It was obtained from Jackson ImmunoResearchLaboratories, INC (ref. 009-000-008).

SELEX Protocol

During the course of the SELEX, continuously decreasing amounts ofhighly pure Human IgG, Fc fragment was incubated with the ssDNAlibrary/pool at decreasing concentrations using as selection buffer 50mM MES pH 5.50, 150 mM NaCl, 5 mM MgCl₂ at decreasing incubation times(see table of FIG. 8).

The unbound ssDNA was partitioned from IgG-Fc/ssDNA complexes usingnitrocellulose filters. The complex containing filters were washed withselection buffer during round 1, 2, & 3 and wash buffer containing 50 mMMOPS pH 5.50, 500 mM NaCl, 5 mM MgCl2 during round 4 to 6 and washbuffer containing 50 mM MOPS pH 5.50, 1M NaCl, 5 mM MgCl2 during round 7& 8 (see table of FIG. 8). After washing, the bound ssDNA was elutedusing elution buffer (50 mM Tris-HCl pH 7.40, 200 mM EDTA).

Before every round (except the first round) a counter selection step wasperformed by incubating the ssDNA pool with one nitrocellulose filter inorder to prevent the enrichment of anti-nitrocellulose aptamers.

The parameters of the SELEX protocols are depicted in FIG. 8.

Determination of the Binding Affinity of the Identified Aptamers by SPR:

The selected aptamer was synthetized with Biotin and a triethyleneglycol spacer at the 5′ end of the oligonucleotide. A 1 μM solution ofthe aptamer was prepared using the SELEX selection buffer. The aptamersolution was heated to 90° C. for 5 min, incubated on ice for 5 min andequilibrated to room temperature for 10 min The preparation was injectedon a streptavidin coated sensor chip SA of Biacore T200 instrument (GEHealthcare) at a flow rate of 10 μl/min for 7 min Then, differentconcentrations of the target (Human polyclonal IgG, purified from humanplasma with a purity of >95%) were injected to the immobilised aptamerat 30 μl/min for 1 minute. After dissociation for 1-2 min a wash stepwas performed by injecting a suitable wash buffer at 30μ1/min for 1 minFor elution, a suitable elution buffer was injected at 30 μl/min for 1-2min Finally the sensor chip was regenerated by injection of 50 mM NaOHat 30 μl/min for 30 sec. During the course of the experiment theresponse signal was recorded in a sensorgram.

2. Results

The SELEX method of the invention enables to identify several anti-IgGaptamer candidates, among which aptamers of SEQ ID NO:5 and SEQ ID NO:6.The binding ability of aptamers of SEQ ID NO:5 and 6 to IgG was assessedby SPR.

FIG. 9A shows the binding curves of human polyclonal IgG for aptamers ofSEQ ID NO:5 (A6-2) and SEQ ID NO:6 (A6-8) immobilized on a sensor chip.The aptamers were shown to bind to polyclonal IgG at pH 5.5. Theinjection of a buffer solution at pH 5.50 comprising 2M NaCl did notsignificantly induce the elution of human polyclonal IgG. The complexbetween the aptamers and polyclonal IgG was dissociated by increasingthe pH of the buffer. Human polyclonal IgG was then released from thecomplex by an elution buffer at pH 7.40. Similarly to anti-fibrinogenaptamers identified by the method of the invention, the anti-IgGaptamers of the invention specifically bound to their target protein ina pH-dependent manner. The highest binding was obtained for pH 5.30. Thebinding level decreased, with the increase of pH. No significant bindingwas observed for pH higher than pH 6.0 (FIG. 9B).

EXAMPLE 7 Affinity Support and Purification of IgG from Plasma

1. Material and Method

Affinity Support

An affinity support was prepared by grafting aptamers of SEQ ID NO:5(A6-2) comprising a C6 spacer with a terminal amino group at its 5′ endand an inverted deoxy-thymidine at its 3′ end, on NHS-activatedSepharose (GE Healthcare):

1 volume of NHS Sepharose activated gel placed in a column was rinsedwith at least 10 volumes of a cold 0,1M HC1 solution, then equilibratedwith at least 8 volumes of cold 100 mM acetate pH 4.0 solution.

After a 3 min-2000 g centrifugation, the supernatant is removed anddrained gel is re-suspended with 2 volumes of an aptamer in 100 mMacetate pH 7.0 solution. This suspension is incubated at roomtemperature under stirring.

After 2 hours, 1 volume of 200 mM Borate pH 9 is added. This suspensionis incubated at room temperature under stirring for 2H30.

After a 3 min-2000 g centrifugation, the supernatant is removed. Drainedgel is re-suspended in 2 volumes of 0.1M Tris-HCl pH 8.5 solution.Suspension is incubated at +4° C. under stirring overnight.

After incubation, and a 3 min-2000 g centrifugation, the supernatant isremoved. The gel alternatively washed with 2 volumes of 0.1M Sodiumacetate +0.5M NaCl pH4.2 and 2 volumes of a 0.1M Tris-HCl pH 8.5solution. This cycle is repeated once.

After a 3 min-2000 g centrifugation supernatant is removed. Drained gelis re-suspended in 2 volumes of binding buffer.

4 mg of aptamer A6-2 was used to be grafted on 1 ml of resine.

Purification of Polyclonal IgG from Purified Plasma IgG or from Plasma

1.1 ml of affinity support was packed in a Tricorn 5/50 column (GEHeathcare). Purified plasma IgG or plasma were diluted with bindingbuffer to reach a 0.8-1 g/L IgG in final concentration. The pH was thenadjusted to 5.5 with 1M citric acid and then filtered 0.45 μm beforeloading onto the column. Chromatography buffers are described in thefollowing table.

Affinity support grafted with aptamers of SEQ ID NO: 5 (Aptamer A6-2)Binding buffer Buffering agent: MES 50 mM NaCl 150 mM, MgCl₂ 5 mM, pH5.5 Elution buffer Buffering agent: MES 50 mM NaCl 150 mM, MgCl₂ 5 mM,pH 7.4

The linear flow rate used for the chromatography was 100 cm/h, and thequantity of IgG loaded was targeted to be close to the resin capacity(6.5 g/L of resin).

2. Results

The results are shown in FIGS. 10A-10B. FIGS. 10A shows thechromatography profile obtained for the IgG from plasma and pre-purifiedplasma IgG on an affinity support grafted with aptamer of SEQ ID NO:5.Noteworthy, most of the contaminant proteins were not retained on thestationary phase whereas IgG bound to the support. IgGs were eluted byincreasing the pH to 7.4. FIG. 10B shows the analysis by SDS Page of thefractions obtained by chromatography for plasma as starting solution.IgGs were mostly present in the elution fraction (lane 3) whereascontaminant proteins were present in the non-retained fraction (lane 2).The relative purity of the IgG eluted from the affinity column was morethan 95% by SDS-PAGE. The high purity of the elution fractiondemonstrated the high specificity of the aptamer for IgG. The yield ofthe chromatography was 82% from pre-purified IgGs and 66% from plasma.Yield could be increased with loading a quantity of IgG below thecapacity of the resin.

Purification with A6-2 Quantity of IgG in Quantity of IgG in aptamer theloaded material the eluate Yield Purified IgG 6.3 mg 5.2 mg 82% Plasma7.9 mg 5.2 mg 66%

The aptamers identified by the method of the invention thus have bindingproperties suitable for use in protein purification.

1.-15. (canceled)
 16. A method for obtaining an aptamer against aprotein target comprising a histidine-containing surface domain, saidmethod comprising: a) contacting the protein target with a candidatemixture of nucleic acids at a pH promoting the formation of positivecharge on the histidine-containing surface domain of said proteintarget; b) recovering nucleic acids that bind to the protein target,while removing unbound nucleic acids, wherein step b) comprises thesteps of: (i) separating the complex formed in step (a) from unboundnucleic acids, and (ii) releasing the nucleic acids from the complex bydissociation, wherein the dissociation of the complex between the boundnucleic acids and the protein target is performed by increasing the pHat a value higher than the pH used in step a); c) amplifying the nucleicacids obtained in step (b) to yield a candidate mixture of nucleic acidswith increased affinity to the protein target; and d) repeating steps(a), (b), (c) until obtaining one or several aptamers against theprotein target of interest.
 17. The method of claim 16, wherein in stepb), sub-step (ii), dissociation of the complex between the bound nucleicacids and the protein target is performed by increasing the pH of a ΔpHof at least 0.8
 18. The method of claim 16 wherein the pH in step a) isless than 7.0.
 19. The method of claim 16, wherein the pH in step a) isfrom 5.0 to 6.9.
 20. The method of claim 16, wherein the pH in step a)is selected so that the electrostatic surface potential of at least oneof the histidine-containing surface domain of the protein target ispositive.
 21. The method of claim 16, wherein: the protein target has anisoelectric point (pI) of less than 7.5, and/or the protein target isdevoid of any surface domain with positive electrostatic potential at apH of more than 7.0.
 22. The method of claim 16, wherein the proteintarget is selected from the group consisting of fibrinogen,immunoglobulin, Fc fragment, and variants thereof.
 23. The method ofclaim 16, wherein the pH of step (a) is determined by obtaining surfaceelectrostatic potential maps at different pH and selecting a pH thatyields a positive surface potential on at least one histidine-containingsurface domain of the protein target and which is included in the pHstability range of the protein target.
 24. The method of claim 16, whichfurther comprises the step of (i) sequencing an aptamer obtained in step(c); (ii) optionally optimizing the sequence of said aptamer; and (iii)producing the aptamer.
 25. An aptamer obtainable or obtained by themethod as defined in claim
 16. 26. The aptamer of claim 25, wherein theaptamer binds to a protein target comprising a histidine-containingsurface domain in a pH dependent-manner.
 27. The aptamer of claim 26,wherein the aptamer binds to the protein target at an acidic pH butwhich does not bind to the protein target at a pH of more than 7.0. 28.The aptamer of claim 26, wherein the aptamer binds to the protein targetat an acidic pH selected from 5.0 to 6.5, but does not bind to theprotein target at a pH of more than 7.0.
 29. An affinity ligandcomprising an aptamer moiety as defined in claim 25 and at least onemoiety for immobilization onto a support.
 30. An affinity supportcomprising thereon a plurality of aptamers as defined in claim
 25. 31. Amethod for obtaining an aptamer against a protein target, said methodcomprising: (i) determining a pH value promoting positive charges in atleast one surface domain of the protein target, (a) contacting theprotein target with a candidate mixture of nucleic acids at the pHdetermined in step (i) in conditions favorable for binding of theprotein target with nucleic acids having affinity for said targets, (b)recovering nucleic acids which bind to the protein target, whileremoving unbound nucleic acids, (c) amplifying the nucleic acidsobtained in step (b) to yield to a candidate mixture of nucleic acidswith increased affinity to the protein target, and (d) repeating steps(a), (b), (c) until obtaining one or several aptamers against theprotein target of interest.
 32. The method of claim 31, furthercomprising the steps of: determining the presence of ahistidine-containing surface domain in the protein target, and if saiddomain is present, determining a pH value promoting positive charges insaid histidine-containing surface domain.
 33. The method of claim 32,wherein the pH value promoting positive charges is a pH value resultingin a local positive surface electrostatic potential in saidhistidine-containing surface domain.